A toolkit for executing and analyzing biomolecular simulations. This project is not inherently unique, given that other superbly implemented and better- documented examples exist elsewhere. The goal of this package is to be expansive and not bloated, to offer flexibility and not streamline users into one particular way of running analyses.
The flexibility of this package means that most of its functions can be applied on either NumPy arrays or the newly-written class called Structure. The choice is up to the user -- NumPy arrays have the benefit of size and speed. Instances of the Structure class are comprehensive and maintain the integrity of Structure internal coordinates.
Currently, this software provides the ability to read and write CHARMM PSF, DCD, and PDB trajectories. There are also several basic analyses. Users can also connect to VMD for visualization and launch replica exchange jobs with NAMD. This work is ongoing and developed by Chris Lockhart.